Code for Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks https://elifesciences.org/articles/84384
- Model for within-host diversity (1_simulations)
Sequence simulations using a model with within-host diversity: simulate.R
Tree comparison: compareTrees.R
- Phylogenetic inference (2_genomics)
Maximum likelihood tree inference: raxml_ng.sh
- Whole-genome sequence analysis (2_genomics)
Raw reads mapping: align.sh
Variant calling: varCalling.sh, softFilt_vcf_by_bed.py, addFT_pileup.py
Pseudosequence: pseudoseq_pileup.sh, vcf2pseudoseq.py, add_maj_min.py
- Analysis (3_analysis)
Comparison of technical replicates: 1_techReps.R
Pairwise comparison of samples: 2_epiLinks.R
Temporal signal in clusters: 3_clust_signal.R
Transmission inference: transPairs.R, likelihoodSEIR.R, transPairs_heatmap.R, transPairs_network.R